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ASPB 2018Frank Skraly
July 17, 2018
Transporter manipulation in food crops for increased yield
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Yield10 company overview
Yield10 Bioscience (NasdaqCM:YTEN) is developing technologies to enhance global food security• Headquartered in Woburn, MA USA• Oilseeds center of excellence in Saskatoon, Canada
Yield10 brings extensive expertise and a track record in optimizing the flow of carbon in living systems to the agriculture sector to increase yield in key row crops
• Yield10 is targeting step-change (10-20%) increases in seed yield • Technology based on 20 years of cutting-edge crop metabolic engineering research• 15 recent patent applications for increased crop yield • Open innovation business model provides low hurdle for work with Ag majors
Yield10 focuses on its core strengths of advanced bioscience and innovation• Discover and de-risk yield technologies for major North American crops:
corn and the two oilseed crops soybean and canola
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The Yield10 platform
• Increasing crop yield is an extremely complex and challenging problem• Screening thousands of individual plant genes has not delivered commercial yield traits
• However, the sector has used this approach to generate billions of individual data points
• Modifying combinations of genes, metabolic and/or regulatory, will be necessary
• GRAIN’s purpose is to be able to convert vast amounts of data into actionable gene modifications
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REGULATORY MODELING
METABOLIC MODELING
FAST FIELD TESTING
Actionable gene modifications
“GRAIN”(Gene-ranking artificial intelligence network)
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Metabolic modeling
Purely stoichiometric Optimize production of biomass, oil, protein, etc. View optimal metabolism (vs. observed metabolism) Show effects of local metabolic changes on entire plant
Eliminate unrealistic reactions from flux-balance analysis Identify slow/difficult reactions within known metabolism Challenge conventional wisdom
FLUX-BALANCE ANALYSIS
KINETICS/THERMODYNAMICSMETABOLIC MODELING
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Crop Expression Trial Group Location Best seed yield increaseCamelina constitutive field Yield10 Canada 23%
Camelina seed-specific greenhouse Yield10 Canada 24%
Camelina seed-specific field Yield10 Canada 7%
Canola constitutive field Yield10 Canada 13%
Camelina constitutive field Schnell (Mich. St.) U.S. 52%
CCP1 (C3003): Trait that increases seed yield
● Transporter found in some algal species ● Induced at low CO2● Localizes to mitochondrial membrane
What is CCP1?
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CCP1 is helpful in plants during photorespiration
CCP1+
WT
Carbon assimilation in Camelina(mmol m-2 s-1)
low oxygen airData from laboratory of Prof. Danny Schnell (Michigan State Univ.)
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Photorespiration needs predicted by model
Flux-balance analysis, optimizing leaf biomass
What mitochondrial factors should increase during photorespiration?
MITOCHONDRION
Glu
2-OG OAA
Asp Malate
OAA
All of these remove electrons from the mitochondrion
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CCP1 facilitates OAA uptake into mitochondria
Relative OAA uptake in mitochondriaisolated from yeast cells
CCP1+WT
OAA (oxaloacetate)is an electron carrier
2 e ̄
MalateOAAmalate
dehydrogenase
Data from laboratory of Prof. Danny Schnell (Michigan State Univ.)8
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Modeling suggests CCP1 role in optimum yield
NH3
OAA
Gly
Ser
OAAMALATE
MALATE
MALATE OAA
MALATE
OAAGLYCERATE
HYDROXYPYRUVATE
● Collect electrons from mitochondrion and chloroplast● Send to peroxisome or cytosol for hydroxypyruvate reductase (HPR)
CHLOROPLAST
PEROXISOME MITOCHONDRION
MALATE
OAA
Photosynthesis
CCP1
e-
e-
e-
CYTOSOL
HPR1
GLYCERATE
HYDROXYPYRUVATE
HPR2 e-PYRUVATE
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Role of CCP1 during photorespiration in the leaf
● HPR flux must be very high at times during photorespiration● Modeling shows that lack of electron shuttling to HPR means >20% yield loss● Accumulation of photorespiratory intermediates could also be a problem
CCP1 may facilitate photorespiration
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NAD(P)
ΔrG'm ≈ +31.3 kJ/molMalate
NAD(P)H
Oxaloacetate
Can CCP1 benefit seed metabolism?
malate dehydrogenase(MDH)
The TCA cycle must run during sugar metabolism in the seed,but one of its steps is very unfavorable:
Pi
ΔrG'm ≈ +43.5 kJ/molADP
H2O
ATPcompare with
spontaneous ATP formation
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Cultured soybean embryo flux data
apparent flux through MDH
Allen et al., Plant J. 58:220–234 (2009)
Carbon efficiency is already >90%
SUGARS
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Can CCP1 benefit seed metabolism?
CCP1 may increase sink strength, NOT carbon efficiency
MAL
Asp
PYR
PYR
ADP
MAL
ATP
FADH2
OAA
Ac-CoA
PiNADH
ADP
ATP
CIT
MAL OAA CIT
PYR
PEP
2PG
PEP
2PG
2-OG
Pi
CO2
TCA cycle
SUCROSE
CHLOROPLAST
CYTOSOL
MITOCHONDRION
CCP1
MDH
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The reverse glyoxylate shunt (rGS)
2 CO2 + 2 HCO3- → OAA
NET
1
1
1
2
2
2
1
1
1
1
What if we could eliminate
photorespirationaltogether?
CO2HCO3─
RELATIVE FLUXES
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Yield10 rGS data
Camelina greenhouse study: Best plants
Maximum relative theoretical yield with rGS under photorespiratory conditions = 212%
Malik, M.R., Tang, J., Sharma, N. et al. Plant Cell Rep. (2018). https://doi.org/10.1007/s00299-018-2308-315
WT100%
228%
173%
216%G
ram
s per
Pla
nt
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Summary
• Yield10 uses modeling and experimentation to identify and de-risk yield gene traits
• Metabolic modeling is a key part of this – but needs to be validated with results
• C3003 (CCP1) has shown significant oilseed yield increases in field trials
• Modeling has helped to explain its role and to suggest further targets
• The reverse glyoxylate shunt (rGS) pathway doubles seed yield in greenhouse studies,
demonstrating that improving carbon conversion efficiency has high yield potential
• Top rGS yield increases agree with model’s predictions
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